Multiple sequence alignment - TraesCS3B01G075500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G075500 chr3B 100.000 2549 0 0 1 2549 46396248 46393700 0 4708
1 TraesCS3B01G075500 chr3B 95.775 568 24 0 1 568 47098917 47099484 0 917
2 TraesCS3B01G075500 chr1B 95.528 1990 80 6 567 2549 581717563 581715576 0 3173
3 TraesCS3B01G075500 chr1B 95.372 1988 85 6 564 2549 520844123 520842141 0 3155
4 TraesCS3B01G075500 chr1B 95.264 1985 87 6 568 2549 671392209 671394189 0 3138
5 TraesCS3B01G075500 chr2B 95.521 1987 80 6 567 2549 458657421 458659402 0 3168
6 TraesCS3B01G075500 chr2B 95.558 1981 83 5 569 2549 667899785 667897810 0 3166
7 TraesCS3B01G075500 chr2B 95.423 1988 81 7 567 2549 692955895 692957877 0 3158
8 TraesCS3B01G075500 chr6B 95.375 1989 83 8 566 2549 478999962 479001946 0 3155
9 TraesCS3B01G075500 chr4A 95.416 1985 83 6 569 2549 705529252 705527272 0 3155
10 TraesCS3B01G075500 chr7B 95.322 1988 83 8 568 2549 720989191 720987208 0 3147
11 TraesCS3B01G075500 chr7D 95.423 568 26 0 1 568 422774807 422775374 0 905
12 TraesCS3B01G075500 chr7D 95.423 568 26 0 1 568 448820842 448821409 0 905
13 TraesCS3B01G075500 chr7D 95.423 568 26 0 1 568 498340713 498341280 0 905
14 TraesCS3B01G075500 chr4D 95.423 568 26 0 1 568 5859108 5859675 0 905
15 TraesCS3B01G075500 chr3D 95.423 568 26 0 1 568 446432027 446431460 0 905
16 TraesCS3B01G075500 chr2D 95.423 568 26 0 1 568 333436106 333436673 0 905
17 TraesCS3B01G075500 chr1D 95.423 568 26 0 1 568 451902140 451902707 0 905
18 TraesCS3B01G075500 chr6D 95.246 568 27 0 1 568 224203175 224202608 0 900


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G075500 chr3B 46393700 46396248 2548 True 4708 4708 100.000 1 2549 1 chr3B.!!$R1 2548
1 TraesCS3B01G075500 chr3B 47098917 47099484 567 False 917 917 95.775 1 568 1 chr3B.!!$F1 567
2 TraesCS3B01G075500 chr1B 581715576 581717563 1987 True 3173 3173 95.528 567 2549 1 chr1B.!!$R2 1982
3 TraesCS3B01G075500 chr1B 520842141 520844123 1982 True 3155 3155 95.372 564 2549 1 chr1B.!!$R1 1985
4 TraesCS3B01G075500 chr1B 671392209 671394189 1980 False 3138 3138 95.264 568 2549 1 chr1B.!!$F1 1981
5 TraesCS3B01G075500 chr2B 458657421 458659402 1981 False 3168 3168 95.521 567 2549 1 chr2B.!!$F1 1982
6 TraesCS3B01G075500 chr2B 667897810 667899785 1975 True 3166 3166 95.558 569 2549 1 chr2B.!!$R1 1980
7 TraesCS3B01G075500 chr2B 692955895 692957877 1982 False 3158 3158 95.423 567 2549 1 chr2B.!!$F2 1982
8 TraesCS3B01G075500 chr6B 478999962 479001946 1984 False 3155 3155 95.375 566 2549 1 chr6B.!!$F1 1983
9 TraesCS3B01G075500 chr4A 705527272 705529252 1980 True 3155 3155 95.416 569 2549 1 chr4A.!!$R1 1980
10 TraesCS3B01G075500 chr7B 720987208 720989191 1983 True 3147 3147 95.322 568 2549 1 chr7B.!!$R1 1981
11 TraesCS3B01G075500 chr7D 422774807 422775374 567 False 905 905 95.423 1 568 1 chr7D.!!$F1 567
12 TraesCS3B01G075500 chr7D 448820842 448821409 567 False 905 905 95.423 1 568 1 chr7D.!!$F2 567
13 TraesCS3B01G075500 chr7D 498340713 498341280 567 False 905 905 95.423 1 568 1 chr7D.!!$F3 567
14 TraesCS3B01G075500 chr4D 5859108 5859675 567 False 905 905 95.423 1 568 1 chr4D.!!$F1 567
15 TraesCS3B01G075500 chr3D 446431460 446432027 567 True 905 905 95.423 1 568 1 chr3D.!!$R1 567
16 TraesCS3B01G075500 chr2D 333436106 333436673 567 False 905 905 95.423 1 568 1 chr2D.!!$F1 567
17 TraesCS3B01G075500 chr1D 451902140 451902707 567 False 905 905 95.423 1 568 1 chr1D.!!$F1 567
18 TraesCS3B01G075500 chr6D 224202608 224203175 567 True 900 900 95.246 1 568 1 chr6D.!!$R1 567

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
296 297 0.659427 TAGTACGAGATTCGGTGGCG 59.341 55.0 3.37 0.0 45.59 5.69 F
509 510 1.260544 GTGGGACCCAACGTACTACT 58.739 55.0 16.98 0.0 33.98 2.57 F
1130 1133 0.880278 CACACACCGAGGAACCACAG 60.880 60.0 0.00 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1104 1107 0.031585 TCCTCGGTGTGTGAGAAACG 59.968 55.000 0.0 0.0 35.43 3.60 R
1361 1364 1.207791 GCCCTCCATCTCTTCTTCCA 58.792 55.000 0.0 0.0 0.00 3.53 R
2035 2046 2.032620 CCATCTGTCCTAGCGGTTACT 58.967 52.381 0.0 0.0 0.00 2.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 2.813179 GCATGGAGCGCAACTACGG 61.813 63.158 11.47 0.00 27.93 4.02
167 168 6.183360 TGTTGCGTTTAGAGACAAAAATCAGT 60.183 34.615 0.00 0.00 0.00 3.41
169 170 5.295787 TGCGTTTAGAGACAAAAATCAGTGT 59.704 36.000 0.00 0.00 0.00 3.55
230 231 1.545582 CCAATGTACTTGCACCTTGGG 59.454 52.381 0.00 0.00 39.31 4.12
288 289 4.164604 AGACAGAGGGAGTAGTACGAGATT 59.835 45.833 0.00 0.00 0.00 2.40
296 297 0.659427 TAGTACGAGATTCGGTGGCG 59.341 55.000 3.37 0.00 45.59 5.69
319 320 6.454583 GCGCACTAACTTATGTCGAATACAAA 60.455 38.462 0.30 0.00 42.70 2.83
509 510 1.260544 GTGGGACCCAACGTACTACT 58.739 55.000 16.98 0.00 33.98 2.57
669 670 3.690280 TCCATGCGCACCGACTCA 61.690 61.111 14.90 0.00 0.00 3.41
820 821 2.689553 TTGAGCATAGATCCGTTGCA 57.310 45.000 12.87 0.00 38.84 4.08
876 879 2.258591 GGCGACAGAGAGCACGAA 59.741 61.111 0.00 0.00 34.54 3.85
1068 1071 1.609061 CGTGTGGAGATGCCTGTCTTT 60.609 52.381 0.00 0.00 37.63 2.52
1104 1107 2.602322 GGCGAGCATTGATCGGAGC 61.602 63.158 23.91 8.82 41.94 4.70
1130 1133 0.880278 CACACACCGAGGAACCACAG 60.880 60.000 0.00 0.00 0.00 3.66
1281 1284 1.078918 CGATGCTCTGGCCAAGACA 60.079 57.895 7.01 5.15 37.74 3.41
1300 1303 6.246420 AGACACTGATAAATGAACTGCAAC 57.754 37.500 0.00 0.00 0.00 4.17
1309 1312 5.710513 AAATGAACTGCAACAAGAGCATA 57.289 34.783 0.00 0.00 41.82 3.14
1315 1318 1.733912 TGCAACAAGAGCATAGCGAAG 59.266 47.619 0.00 0.00 37.02 3.79
1349 1352 2.518349 CCAAACCACAGTGGCCGT 60.518 61.111 20.48 2.06 42.67 5.68
1431 1434 5.474532 TGTTGAGCTTAGCATGTTGAAGAAT 59.525 36.000 7.07 0.00 0.00 2.40
1739 1743 6.624352 TGCAGCTAATGAATTATTCCAGAC 57.376 37.500 2.22 0.00 0.00 3.51
1885 1890 5.127356 AGCTCTGGTAGATGTTTACACCTAC 59.873 44.000 5.94 5.94 32.04 3.18
1893 1898 5.003804 AGATGTTTACACCTACTGCCAAAG 58.996 41.667 0.00 0.00 0.00 2.77
2035 2046 1.078708 GGTGTTTAGGGCTGCGCTA 60.079 57.895 20.82 20.82 0.00 4.26
2189 2205 1.434555 CAAGACCGCGTGGATTTGTA 58.565 50.000 24.59 0.00 39.21 2.41
2463 2479 5.048573 GGCACTTGGTTTAGGATTTAAACGA 60.049 40.000 0.00 0.00 38.06 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 6.974965 ACTTTGATTTCTTGACTGATCAACC 58.025 36.000 0.00 0.0 40.01 3.77
167 168 3.505680 CGGTCATTCCTCCAATCAAAACA 59.494 43.478 0.00 0.0 0.00 2.83
169 170 3.088532 CCGGTCATTCCTCCAATCAAAA 58.911 45.455 0.00 0.0 0.00 2.44
230 231 1.449778 GTTAGAAGGTGGAGCGGGC 60.450 63.158 0.00 0.0 0.00 6.13
237 238 6.309737 GTGTAATAAGTCACGTTAGAAGGTGG 59.690 42.308 13.47 0.0 43.08 4.61
288 289 0.533491 ATAAGTTAGTGCGCCACCGA 59.467 50.000 4.18 0.0 34.49 4.69
296 297 7.373441 GCATTTGTATTCGACATAAGTTAGTGC 59.627 37.037 0.00 0.0 38.07 4.40
368 369 1.964223 TGATCCCTCTATTCGCTCACC 59.036 52.381 0.00 0.0 0.00 4.02
509 510 3.544698 AGTCACCTTACCTCTCTCCAA 57.455 47.619 0.00 0.0 0.00 3.53
669 670 2.808543 GAGACGCCAAAGTTCACAGAAT 59.191 45.455 0.00 0.0 0.00 2.40
800 801 3.136763 CTGCAACGGATCTATGCTCAAT 58.863 45.455 15.41 0.0 40.66 2.57
851 854 0.463204 CTCTCTGTCGCCATGGTCAT 59.537 55.000 14.67 0.0 0.00 3.06
876 879 3.753434 CTCTCGCCGTGGTCAGCT 61.753 66.667 0.00 0.0 0.00 4.24
907 910 1.229658 AGCTAGCTTCCCACCACCT 60.230 57.895 12.68 0.0 0.00 4.00
940 943 0.545309 TCCACAGCTAGCTTCCCACT 60.545 55.000 16.46 0.0 0.00 4.00
1068 1071 2.889617 CGGCACCACGGATAGACA 59.110 61.111 0.00 0.0 0.00 3.41
1093 1096 2.271800 GTGAGAAACGCTCCGATCAAT 58.728 47.619 0.00 0.0 43.26 2.57
1104 1107 0.031585 TCCTCGGTGTGTGAGAAACG 59.968 55.000 0.00 0.0 35.43 3.60
1281 1284 6.569226 GCTCTTGTTGCAGTTCATTTATCAGT 60.569 38.462 0.00 0.0 0.00 3.41
1300 1303 1.667724 CAACCCTTCGCTATGCTCTTG 59.332 52.381 0.00 0.0 0.00 3.02
1361 1364 1.207791 GCCCTCCATCTCTTCTTCCA 58.792 55.000 0.00 0.0 0.00 3.53
1419 1422 7.337942 AGCTTCCTAACCTTATTCTTCAACATG 59.662 37.037 0.00 0.0 0.00 3.21
1431 1434 6.620877 TGATCTTCAAGCTTCCTAACCTTA 57.379 37.500 0.00 0.0 0.00 2.69
1584 1587 7.117667 GGCCAACATTTAAACTAGGTGAATTTG 59.882 37.037 0.00 0.0 0.00 2.32
1674 1678 9.794685 GTTTCTGAATTATTCATTTCTTCTCCC 57.205 33.333 8.17 0.0 39.30 4.30
1946 1956 3.390639 TGTGCATTTTCCACCCTTCATTT 59.609 39.130 0.00 0.0 32.30 2.32
2035 2046 2.032620 CCATCTGTCCTAGCGGTTACT 58.967 52.381 0.00 0.0 0.00 2.24
2298 2314 3.188254 CGTGTGCAAACATTCATGGTCTA 59.812 43.478 8.00 0.0 0.00 2.59


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.